Natural variation in Arabidopsis thaliana and its importance to the study of genomics

Augustus Amato, Courtney Currier, Julia Kohn, Ashley Markowski

Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556

Introduction Results Conclusions

The use of model systems in biology provides one substantial way to
•Glabrous samples produced two bands; wild-type produced one band. Thanks to this experiment, natural variation within genomes is becoming
understand genomics in natural variation, and Arabidopsis thaliana is perhaps
•Lane 6 appears to have two bands, but the second, lighter one is due to contamination. more easily recognizable for genomics as a whole based on the methods
the most ideal. As an obligate self-pollinator, using A. thaliana as a model for
•The glabrous mutation is a deletion; it traveled farther, meaning it was a smaller DNA used. One basic procedure for identifying loci on chromosomes responsible
genomics allows for quicker reproduction, increasing the efficiency of the
fragment. for mutations, or variation, is genetic mapping (Borevitz, 2003). On this
experiment. In addition to this factor, A. thaliana has a relatively small
•Our results were consistent with class data in that the glabrous produced two bands and note, A. thaliana is an ideal model organism that can be used in linkage
genome consisting of only five chromosomes, whereas most other plants may
wild-type produced one. mapping to discern the loci contributing to variation. These loci are called
contain up to ten thousand times as much DNA. As a result, the entire A.
quantitative trait loci (QTL). This is where sequencing A. thaliana finds
thaliana genome has been sequenced from this efficient and hardy plant.
relevance in this experiment; through the experimental methods, the locus
Similarly, A. thaliana is ideal in sequencing because of its recognizable traits;
responsible for the glabrous mutation was identified, and the method is used
specifically, this experiment maps the glabrous and wild-type genes of the
as a model today for more complex organisms.
plant. Because of its simple structure, its accessibility, and its size, A.
An inevitable factor in the study of genomics is natural variation.
thaliana was used as this experiment’s scientific model.
Natural variation assumes all forms of mutations and glitches in DNA
Because the general process from sequencing the genome of A. thaliana
replication during an organism’s life, therefore affecting the overall genome
has already been determined, the focus of understanding the process itself is Lab gel showing wild-type and glabrous for subsequent generations. Over time, these mutations compose gradual
vital to this experiment. It has been established that sequencing is a difficult, A. thaliana genes changes that become noticeable, accounting for evolutionary occurrences.
yet important, procedure. This experiment aims to use A. thaliana as an easy
The glabrous mutation in A. thaliana is evidence of this phenomenon. The
model to sequence, thus allowing for the development of a method to make
study of natural variation is essential in understanding evolutionary biology
the genomic sequencing of other organisms possible; the genetic sequencing
and the source of complex traits in any organism, traits that, once sequenced
for A. thaliana, which is relatively easy, provides researchers an entryway
in a genome, lead scientists to biological answers in all fields of research.
into the world of genetic sequencing while revealing how difficult this task
can be.

Literature cited
The A. thaliana Initiative. “Representation of the A. thaliana
Figure 3. The sequenced A. thaliana genome. chromosomes.” Photo.
Borevitz, Justin O. and Magnus Nordborg. 2003. The Impact of Genomics
Materials and methods on the Study of Natural Variation in A. thaliana. Plant Physiology
132: 718-725.
We followed a modified Edvotek isolation kit protocol (Dan Borkowski). Chromosome Map Tool. The A. thaliana Information Resource (Tair). 10
After a week of growth, glabrous and wild-type A. thaliana plants were July 2009. Carnegie Institution of Washington Department of Plant
harvested for DNA extraction (Fig. 1). Biology. 3 Dec. 2009
3-4 plants per sample were coarsely ground
Figure 2. Lanes 2,3, and 5 contain glabrous A. thaliana DNA, <http://www.A.thaliana.org/jsp/ChromosomeMap/tool.jsp>
while lane 6 contains wild-type.
with mortar and pestle, mixed with extraction Niemi, Kevin. “A. thaliana thaliana.” Photo. Wisconsin Teacher
buffer and NaCl solution, and centrifuged to Enhancement Program. 18 Feb. 2009. 3 Dec. 2009
separate DNA from unwanted plant materials. <http://wistep.wisc.edu/researchstudents.html>
Cold isopropanol alcohol was mixed with the Figure 4. The location of the glabrous gene. Nature.com. 15 Nov. 2000. 3 Dec. 2009
supernatant; this mixture was chilled and then http://www.nature.com/nature/journal/v408/n6814/full/408796a 0.html
centrifuged again to precipitate the DNA. The
Figure 1. Wild-type A.
resulting pellet was washed in ethanol, dried, thaliana plant. Note the
and then suspended in TE buffer for storage. presence of hairs on the
leaves; these are absent in The glabrous samples had two bands, signifying a mutation compared to the wild type,
Edvotek PCR pelletM was combined with glabrous plants. which had one band (Fig. 2). This second band traveled farther than the first band, which
distilled water, primer mix, and extracted A. thaliana DNA. This was means that it is a smaller DNA fragment, making it a deletion. This deletion is 700 base
subjected to 35 rounds of PCR thermocycling. pairs long. It accounts for the loss of the fine glandular hairs (trichomes) normally on the
Acknowledgments
After the addition of loading dye, the resulting DNA was run for an surface of the glabrous A. thaliana leaf. Consequently, this mutation is a type of natural We thank Daniel Borkowski for laboratory guidance and Mark Olsen for
hour in an ethidium bromide-treated agarose gel using TAE buffer. The variation in the plant. A. thaliana has a very small genome; therefore, its nucleotide assistance on creating a research presentation. We also thank the University
DNA bands were identified via exposure to ultraviolet light. sequence can be determined compared to other larger genomes, providing a genetic basis of Notre Dame for access to both greenhouse and laboratory resources and
for its phenotype. for funding materials.